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Old 11-26-2013, 06:48 AM   #1
sindrle
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Default Running out of disk space with BWA, wrong CMD line?

Hi!
I keep getting "out of disk space" errors , even with 800gb free space.

This is my code:

bwa samse -n4 reference.fa x.sai x.fastq.gz > x.sam

Somebody knows?
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Old 11-26-2013, 07:00 AM   #2
GenoMax
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Have you checked to see if your /tmp is filling up? Are these very large files?
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Old 11-26-2013, 07:03 AM   #3
sindrle
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Thats probably it..

All files is about 2-3gb. The x.sam file will be 16gb I guess..

Could I compress the sam to bam like this?

bwa samse -n4 reference.fa x.sai x.fastq.gz > x.sam | samtools view -Sb > x.bam

Last edited by sindrle; 11-26-2013 at 07:07 AM.
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Old 11-26-2013, 07:14 AM   #4
GenoMax
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See this thread for examples of piping: http://www.biostars.org/p/43677/
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